Greetings, all

I have a quick question regarding the example in the edgeR users manual in section 3.2.6 which describes the ANOVA-like tests for multiple comparisons. In the example there are three groups, namely A, B and C with the design matrix using C as the reference group (this is the "design2" matrix). I would just like to know exactly what comparisons are being done when we specify "coef = 2:3". I understand the comparisons of "A-C" and "B-C" are both being done, but is "B-A" or "A-B" also being done? It seems like it should since the authors also state that it doesn't matter which group is used as the reference level.

My own data has four separate groups and I would like to run a similar type of test so, I would like to be absolutely certain, perhaps for own sanity more than anything.

Thank you in advance.